Thanks for the welcome. I came up with that SOP for a Star Trek version of FT that didn't have PD and allowed any weapons to hit fighters with a -1 penalty (sound familiar). I'll try it with Starmada and let you know what I think.
A good compromise may be letting anti-fighter weapons and seekers defend ships during the Fighter Phase. Perhaps even nearby ships within range (escorts). So the Fighter Phase would be something like 1) move fighters 2) resolve ship defenses 3) fighters attack.
I'm a big Trek fan and since I have all the minis and rules, that's the universe we play in. Anyway, I modified phasers a bit from their KA and RA descriptions. Phaser Is are 15,1/3+/1/1; phaser III's : 3,2/5+/1/1, Anti-Fighter. I might try the above Fighter Phase sequence to see if it is the right flavor. Marc may be right though and it may reduce to much the combat effectiveness of fighters/seekers.